Life Sciences Commons^™

Plant Sex And The Evolution Of Plant Defenses Against Herbivores, Marc T.J. Johnson, Stacey Dewitt Smith, Marc D. Rausher, Douglas J. Futuyma

School of Biological Sciences: Faculty Publications

Despite the importance of plant–herbivore interactions to the ecology and evolution of terrestrial ecosystems, the evolutionary factors contributing to variation in plant defenses against herbivores remain unresolved. We used a comparative phylogenetic approach to examine a previously untested hypothesis (Recombination-Mating System Hypothesis) that posits that reduced sexual reproduction limits adaptive evolution of plant defenses against arthropod herbivores. To test this hypothesis we focused on the evening primrose family (Onagraceae), which includes both sexual and functionally asexual species. Ancestral state reconstructions on a 5-gene phylogeny of the family revealed between 18 and 21 independent transitions between sexual and asexual reproduction. Based …

Species-Driven Changes In Nitrogen Cycling Can Provide A Mechanism For Plant Invasions, Johannes M. H. Knops, Ramesh Laungani

School of Biological Sciences: Faculty Publications

Traits that permit successful invasions have often seemed idiosyncratic, and the key biological traits identified vary widely among species. This fundamentally limits our ability to determine the invasion potential of a species. However, ultimately, successful invaders must have positive growth rates that longer term result in higher biomass accumulation than competing established species. In many terrestrial ecosystems nitrogen limits plant growth, and is a key factor determining productivity and the outcome of competition among species. Plant nitrogen use may provide a powerful framework to evaluate the invasive potential of a species in nitrogen-limiting ecosystems. Six mechanisms influence plant nitrogen use …

Similar Patterns Of Linkage Disequilibrium And Nucleotide Diversity In Native And Introduced Populations Of The Pea Aphid, Acyrthosiphon Pisum, Jennifer A. Brisson, Sergey V. Nuzhdin, David L. Stern

School of Biological Sciences: Faculty Publications

Background: The pea aphid, Acyrthosiphon pisum, is an emerging genomic model system for studies of polyphenisms, bacterial symbioses, host-plant specialization, and the vectoring of plant viruses. Here we provide estimates of nucleotide diversity and linkage disequilibrium (LD) in native (European) and introduced (United States) populations of the pea aphid. Because introductions can cause population bottlenecks, we hypothesized that U.S. populations harbor lower levels of nucleotide diversity and higher levels of LD than native populations. Results: We sampled four non-coding loci from 24 unique aphid clones from the U. S. (12 from New York and 12 from California) and 24 …

Transcriptional Profiling Of The Sperm Storage Organs Of Drosophila Melanogaster, Adrianne M. Prokupek, Stephen D. Kachman, Istvan Ladunga, Lawrence G. Harshman

School of Biological Sciences: Faculty Publications

The occurrence of female sperm storage across taxa indicates the importance of this complex and dynamic process. Organs responsible for sperm storage (SSOs) and proteins expressed therein, are important in fundamental aspects of reproduction and could play a major role in evolutionary processes such as post-mating sexual selection. Given the essential role of SSOs, it is surprising that the process of sperm storage is so poorly understood. This study investigated the transcriptome of female Drosophila melanogaster SSOs (seminal receptacle and spermathecae). Spermathecae were enriched for proteases and metabolic enzymes while the seminal receptacle was enriched for genes involved in localization, …

Natural Genetic Variation In Transcriptome Reflects Network Structure Inferred With Major Effect Mutations: Insulin/Tor And Associated Phenotypes In Drosophila Melanogaster, Sergey V. Nuzhdin, Jennifer A. Brisson, Andrew Pickering, Marta L. Wayne, Lawrence G. Harshman, Lauren M. Mcintyre

School of Biological Sciences: Faculty Publications

Background: A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation reshapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results: We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. …

Wnt And Egf Pathways Act Together To Induce C. Elegans Male Hook Development, Hui Yu, Adeline Seah, Michael A. Herman, Edwin L. Ferguson, H. Robert Horvitz, Paul W. Sternberg

School of Biological Sciences: Faculty Publications

Comparative studies of vulva development between Caenorhabditis elegans and other nematode species have provided some insight into the evolution of patterning networks. However, molecular genetic details are available only in C. elegans and Pristionchus pacificus. To extend our knowledge on the evolution of patterning networks, we studied the C. elegans male hook competence group (HCG), an equivalence group that has similar developmental origins to the vulval precursor cells (VPCs), which generate the vulva in the hermaphrodite. Similar to VPC fate specification, each HCG cell adopts one of three fates (1°, 2°, 3°), and 2° HCG fate specification …

Something Old, Something New, Something Borrowed; How The Thermoacidophilic Archaeon Sulfolobus Solfataricus Responds To Oxidative Stress, Walid S. Maaty, Blake Wiedenheft, Pavel Tarlykov, Nathan Schaff, Joshua Heinemann, Jim Robinson-Cox, Jacob Valenzuela, Amanda Dougherty, Paul H. Blum, C. Martin Lawrence, Trevor Douglas, Mark J. Young, Brian Bothner

School of Biological Sciences: Faculty Publications

To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H2O2) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts …

Crystallization And Crystal-Packing Studies Of Chlorella Virus Deoxyuridine Triphosphatase, Kohei Homma, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an aminoterminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65 A . In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but …

Macroevolutionary Tests Of Pollination Syndromes: A Reply To Fenster Et Al., Stacey Dewitt Smith, Cécile Ané, David A. Baum

School of Biological Sciences: Faculty Publications

Studies of floral ecology and evolution are often centered on the idea that particular floral trait combinations, or syndromes, represent adaptations for particular pollinators. Despite the conceptual importance of pollination syndromes, few macroevolutionary studies have statistically examined the relationship between pollinators and floral traits. Using 15 species of Iochroma, Smith et al. applied phylogenetically structured correlation analyses to test the relationship between floral variation and pollination system, quantified in terms of the importance of major pollinator groups. This study revealed that pollinator shifts are tied to changes in nectar reward and floral display but are not significantly correlated with …

Natural History Note No Trade-Off Between Seed Size And Number In The Valley Oak Quercus Lobata, Walter D. Koenig, Johannes M.H. Knops, William J. Carmen, Richard D. Sage

School of Biological Sciences: Faculty Publications

We examined the relationship between acorn mass and number in valley oaks (Quercus lobata) over 4 years in central coastal California. Despite considerable variation in acorn size among both trees and years, trees produced acorns of the same size relative to other trees in different years. Across years, the relationship between acorn mass and acorn crop size was generally positive, even after controlling for environmental conditions and differences in individual tree size and quality. Life-history trade-offs in valley oaks are primarily between current and future reproduction and indirectly between concurrent growth and reproduction, not between seed size and …

Arginine-Induced Germ Tube Formation In Candida Albicans Is Essential For Escape From Murine Macrophage Line Raw 264.7, Suman Ghosh, Dhammika H. M. L. P. Navarathna, David D. Roberts, Jake T. Cooper, Audrey L. Atkin, Thomas M. Petro, Kenneth W. Nickerson

School of Biological Sciences: Faculty Publications

The opportunistic fungal pathogen Candida albicans is a part of the normal flora but it also causes systemic candidiasis if it reaches the bloodstream. Upon being phagocytized by macrophages, an important component of innate immunity, C. albicans rapidly upregulates a set of arginine biosynthetic genes. Arginine, urea, and CO2 induced hyphae in a density-dependent manner in wild-type, cph1/cph1, and rim101/rim101 strains but not in efg1/efg1 or cph1/cph1 efg1/efg1 strains. Arginase (Car1p) converts arginine to urea, which in turn is degraded by urea amidolyase (Dur1,2p) to produce CO2, a signal for hyphal switching. We used a dur1,2/dur1,2 mutant (KWN6) and the …

Role Of Vapbc Toxin–Antitoxin Loci In The Thermal Stress Response Of Sulfolobus Solfataricus, Charlotte R. Cooper, Amanda J. Daugherty, Sabrina Tachdjian, Paul H. Blum, Robert M. Kelly

School of Biological Sciences: Faculty Publications

TA (toxin–antitoxin) loci are ubiquitous in prokaryotic microorganisms, including archaea, yet

their physiological function is largely unknown. For example, preliminary reports have suggested

that TA loci are microbial stress-response elements, although it was recently shown that knocking

out all known chromosomally located TA loci in Escherichia coli did not have an impact on

survival under certain types of stress. The hyperthermophilic crenarchaeon Sulfolobus solfataricus

encodes at least 26 vapBC (where vap is virulence-associated protein) family TA loci in its

genome. VapCs are PIN (PilT N-terminus) domain proteins with putative ribonuclease activity,

while VapBs are proteolytically labile proteins, which purportedly function …

Caenorhabditis Elegans Genomic Response To Soil Bacteria Predicts Environment-Specific Genetic Effects On Life History Traits, Joseph D. Coolon, Kenneth L. Jones, Timothy C. Todd, Bryanua C. Carr, Michael A. Herman

School of Biological Sciences: Faculty Publications

With the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. One application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. These experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. However, whether differential expression is predictive of functional importance has yet to be tested. Here we have addressed this expectation by employing Caenorhabditis elegans as a model for the interaction of native soil nematode taxa and …

The Nuclear Receptor Nhr-25 Cooperates With The Wnt/Β-Catenin Asymmetry Pathway To Control Differentiation Of The T Seam Cell In C. Elegans, Martina Hajduskova, Marek Jindra, Michael A. Herman, Masako Asahina

School of Biological Sciences: Faculty Publications

Asymmetric cell divisions produce new cell types during animal development. Studies in Caenorhabditis elegans have identified major signal-transduction pathways that determine the polarity of cell divisions. How these relatively few conserved pathways interact and what modulates them to ensure the diversity of multiple tissue types is an open question. The Wnt/β-catenin asymmetry pathway governs polarity of the epidermal T seam cell in the C. elegans tail. Here, we show that the asymmetry of T-seam-cell division and morphogenesis of the male sensory rays require NHR-25, an evolutionarily conserved nuclear receptor. NHR-25 ensures the neural fate of the T-seam-cell descendants in cooperation …

Ecological Genomics Of Nematode Community Interactions: Model And Non-Model Approaches, Michael A. Herman, Joseph D. Coolon, Kenneth L. Jones, Timothy Todd

School of Biological Sciences: Faculty Publications

The effects of human-induced environmental change are evident at multiple levels of biological organization. To date, most environmental change studies have focused on effects at the ecosystem, community, and organismal levels. However, the ultimate controls of biological responses are located in the genome. Thus, genetic and genomic studies of organismal responses to environmental changes are necessary. Recent advances in genome analysis now make such analyses possible. In this chapter we describe a research approach and program that can begin to span this gap by using genome-enabled approaches to characterize organismal changes and then employing a genetically tractable model organism to …

The Impact Of Co-Occurring Tree And Grassland Species On Carbon Sequestration And Potential Biofuel Production, Ramesh Laungani, Johannes Knops

School of Biological Sciences: Faculty Publications

We evaluated how three co-occurring tree and four grassland species influence potentially harvestable biofuel stocks and above- and belowground carbon pools. After 5 years, the tree Pinus strobus had 6.5 times the amount of aboveground harvestable biomass as another tree Quercus ellipsoidalis and 10 times that of the grassland species. P. strobus accrued the largest total plant carbon pool (1375 gCm -2 or 394 gCm -2 yr), while Schizachyrium scoparium accrued the largest total plant carbon pool among the grassland species (421 gCm -2 or 137 gCm -2 yr). Quercus ellipsoidalis accrued 850 gCm -2, Q. macrocarpa 370 gCm -2, …

Physiological And Taxonomic Description Of The Novel Autotrophic, Metal Oxidizing Bacterium, Pseudogulbenkiania Sp. Strain 2002, Karrie A. Weber, David B. Hedrick, Aaron D. Peacock, J. Cameron Thrash, David C. White, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

A lithoautotrophic, Fe(II) oxidizing, nitratereducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as part of a study on nitrate-dependent Fe (II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium which tested positive for oxidase, catalase, and urease. Analysis of the complete 16S rRNA gene sequence placed strain 2002 in a clade within the family Neisseriaceae in the order Nessieriales of the Betaproteobacteria 99.3% similar to Pseudogulbenkiania subflava. Similar to P. sublfava, predominant whole cell fatty acids were …

Long 3’-Utrs Target Wild-Type Mrnas For Nonsense-Mediated Mrna Decay In Saccharomyces Cerevisiae, Bessie W. Kebaara, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

The nonsense-mediated mRNA decay (NMD) pathway,

present in most eukaryotic cells, is a specialized

pathway that leads to the recognition and rapid

degradation of mRNAs with premature termination

codons and, importantly, some wild-type

mRNAs. Earlier studies demonstrated that aberrant

mRNAs with artificially extended 3’-untranslated

regions (3’-UTRs) are degraded by NMD. However,

the extent to which wild-type mRNAs with long

3’-UTRs are degraded by NMD is not known.

We used a global approach to identify wild-type

mRNAs in Saccharomyces cerevisiae that have

longer than expected 3’-UTRs, and of these

mRNAs tested, 91% were degraded by NMD. We

demonstrate for the first …

Evolution And Pleiotropy Of Trithorax Function In Arabidopsis, Zoya Avramova

School of Biological Sciences: Faculty Publications

The SET domain-containing genes of the TRITHORAX family encode epigenetic factors that maintain the expression of targeted genes. Trithorax homologs have been found in both animals and plants. Since these are thought to have evolved multicellularity independently, common mechanisms of epigenetic regulation must be evolutionarily ancient and derived from a common ancestor. In addition, each lineage has evolved unique mechanisms to expand the original repertoire of epigenetic functions. Phylogenetic analysis of SET domain proteins has outlined some intriguing evolutionary trends. In plants, epigenetic gene silencing mechanisms have been aggressively pursued. In contrast, studies of epigenetic mechanisms maintaining active gene expression …

Interactive Effects Of Time, Co2, N, And Diversity On Total Belowground Carbon Allocation And Ecosystem Carbon Storage In A Grassland Community, E. Carol Adair, Peter B. Reich, Sarah E. Hobbie, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Predicting if ecosystems will mitigate or exacerbate rising CO2 requires understanding how elevated CO₂ will interact with coincident changes in diversity and nitrogen (N) availability to affect ecosystem carbon (C) storage. Yet achieving such understanding has been hampered by the difficulty of quantifying belowground C pools and fluxes. Thus, we used mass balance calculations to quantify the effects of diversity, CO₂, and N on both the total amount of C allocated belowground by plants (total belowground C allocation, TBCA) and ecosystem C storage in a periodically burned, 8-year Minnesota grassland biodiversity, CO₂, and N experiment …

Occurrence Of Trichosirocalus Horridus (Coleoptera: Curculionidae) On Native Cirsium Altissimum Versus Exotic C. Vulgare In North American Tallgrass Prairie, Masaru Takahashi, Svata M. Louda, Tom E. X. Miller, Charles W. O'Brien

School of Biological Sciences: Faculty Publications

Postrelease studies can provide data with which to evaluate expectations based on prerelease tests of biological control insects. In 2004, we observed Trichosirocalus horridus Panzer (Coleoptera: Curculionidae), the rosette weevil introduced into North America against Eurasian thistles, feeding on native tall thistle, Cirsium altissimum L. Spreng., in tallgrass prairie. In this study, we examined the rosette weevil's use of tall thistle, compared with its use of the co-occurring exotic bull thistle, C. vulgare (Savi) Tenore. For both thistle species, we quantified weevil frequency, abundance, and seasonal variation in incidence, using both timed observations at two sites over two growing seasons …

Impacts Of Insect Herbivory On Cactus Population Dynamics: Experimental Demography Across An Environmental Gradient, Tom E. X. Miller, Svata M. Louda, Karen A. Rose, James O. Eckberg

School of Biological Sciences: Faculty Publications

Understanding the role of consumers in plant population dynamics is important, both conceptually and practically. Yet, while the negative effects of herbivory on plant performance have been well documented, we know much less about how individuallevel damage translates to impacts on population growth or whether spatial variation in herbivory affects patterns of plant distribution. We studied the role of insect herbivory in the dynamics and distribution of the tree cholla cactus (Opuntia imbricata), a long-lived perennial plant, across an elevational gradient in central New Mexico, USA, from low-elevation grassland (1670 m) to a grassland–mountain transition zone (1720 m) …

Computational Prediction Of Novel Non-Coding Rnas In Arabidopsis Thaliana, Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang

School of Biological Sciences: Faculty Publications

Background: Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and Arabidopsis have revealed a great number of transcripts, a large portion of which have little or no capability to encode proteins. This unexpected finding suggests that the currently known repertoire of ncRNAs may only represent a small fraction of ncRNAs of the organisms. Thus, efficient and effective prediction of ncRNAs has become an important task in bioinformatics in recent years. Among the available …

Model Complexity Affects Transient Population Dynamics Following A Dispersal Event: A Case Study With Pea Aphids, Brigitte Tenhumberg, Andrew J. Tyre, Richard Rebarber

School of Biological Sciences: Faculty Publications

Stage-structured population models predict transient population dynamics if the population deviates from the stable stage distribution. Ecologists’ interest in transient dynamics is growing because populations regularly deviate from the stable stage distribution, which can lead to transient dynamics that differ significantly from the stable stage dynamics. Because the structure of a population matrix (i.e., the number of life-history stages) can influence the predicted scale of the deviation, we explored the effect of matrix size on predicted transient dynamics and the resulting amplification of population size. First, we experimentally measured the transition rates between the different life-history stages and the adult …

Behavioral Response Of Dissimilatory Perchlorate-Reducing Bacteria To Different Electron Acceptors, Yvonne Sun, Ruth L. Gustavson, Nadia Ali, Karrie A. Weber, Lacey L. Westphal, John D. Coates

School of Biological Sciences: Faculty Publications

The response behavior of three dissimilatory perchlorate-reducing bacteria to different electron acceptors (nitrate, chlorate, and perchlorate) was investigated with two different assays. The observed response was speciesspecific, dependent on the prior growth conditions, and was inhibited by oxygen. We observed attraction toward nitrate when Dechloromonas aromatica strain RCB and Azospira suillum strain PS were grown with nitrate. When D. aromatica and Dechloromonas agitata strain CKB were grown with perchlorate, both responded to nitrate, chlorate, and perchlorate. When A. suillum was grown with perchlorate, the organism responded to chlorate and perchlorate but not nitrate. A gene replacement mutant in the perchlorate …

Sex Effects On Life Span And Senescence In The Wild When Dates Of Birth And Death Are Unknown, Felix Zajitschek, Chad Brassil, Russell Bonduriansky, Robert C. Brooks

School of Biological Sciences: Faculty Publications

Males and females allocate and schedule reproductive effort in very different ways. Because the timing and amount of reproductive effort influence survival and thus the optimization of life histories, mortality and senescence are predicted to be sex specific. However, age-specific mortality rates of wild animals are often difficult to quantify in natural populations. Studies that report mortality rates from natural populations are, therefore, almost entirely confined to long-lived, easy-to-track species such as large mammals and birds. Here, we employ a novel approach using capture–mark–recapture data from a wild population of black field crickets (Teleogryllus commodus) to test for …

Blood Sampling Reduces Annual Survival In Cliff Swallows (Petrochelidon Pyrrhonota) -- La Toma De Muestras De Sangre Reduce La Supervivencia Anual En Petrochelidon Pyrrhonota, Charles R. Brown, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

Researchers commonly collect blood samples from wild birds, and most workers assume that blood sampling has no adverse effect on the birds’ survival. Few studies, however, have done controlled comparisons among bled and non-bled individuals and estimated survival using modern statistical methodology. We used a data set on Cliff Swallows (Petrochelidon pyrrhonota) that included 2,945 bled and 7,822 non-bled birds captured at the same times and sites in southwestern Nebraska from 1986 to 2006 to estimate annual survival and recapture probabilities of each group. Blood was collected with brachial venipuncture in amounts varying from 0.3% to 1.2% of …